Automatically include sample code into user guide

[mbrukman]

This change add scripts to generate user_guide.md automatically from special markers that are now visible in the source file user_guide.md.in. This allows us to easily keep the source code up-to-date in the docs without having to manually copy-paste the code, and to ensure that the code we test (in the example files) is exactly the code that ends up in the documentation.

Closes #54

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Incidentally, this change also demonstrated that paths to sample files were broken since PR #59, and now that we automatically include them in, such a change would be an error.